Tracking climate-change-induced biological invasions by metabarcoding archived natural eDNA samplers.

In a time of unprecedented environmental change, understanding the response of organisms and ecosystems to change is paramount1. However, our knowledge of anthropogenic impacts on ecosystems is limited by a lack of standardized retrospective biomonitoring data2. Here, we use a four-decade time series of archived blue mussels to trace spatiotemporal biodiversity change in coastal ecosystems. The filter-feeding mussels, which were initially collected for pollution monitoring, can serve as natural eDNA samplers, carrying an imprint of the surrounding aquatic community at the time of sampling3. By sequencing the preserved DNA, we characterize highly diverse mussel-associated communities and reconstruct the invasion trajectory of an invasive species, the barnacle Austrominius modestus. We quantitatively trace population growth of the invader to the detriment of native taxa and uncover repeated population collapses and reinvasions after cold winters. By providing highly resolved temporal data on community assembly and global warming-driven invasion processes, natural eDNA sampler time series overcome a critical shortfall in our understanding of biodiversity change in the Anthropocene.

Molecular diet analysis in mussels and other metazoan filter feeders and an assessment of their utility as natural eDNA samplers.

Molecular gut content analysis is a popular tool to study food web interactions and has recently been suggested as an alternative source for DNA-based biomonitoring. However, the overabundant consumer's DNA often outcompetes that of its diet during PCR. Lineage-specific primers are an efficient means to reduce consumer amplification while retaining broad specificity for dietary taxa. Here, we designed an amplicon sequencing assay to monitor the eukaryotic diet of mussels and other metazoan filter feeders and explore the utility of mussels as natural eDNA samplers to monitor planktonic communities. We designed several lineage-specific rDNA primers with broad taxonomic suitability for eukaryotes. The primers were tested using DNA extracts of different limnic and marine mussel species and the results compared to eDNA water samples collected next to the mussel colonies. In addition, we analysed several 25-year time series samples of mussels from German rivers. Our primer sets efficiently prevent the amplification of mussels and other metazoans. The recovered DNA reflects a broad dietary preference across the eukaryotic tree of life and considerable taxonomic overlap with filtered water samples. We also show the utility of a reversed version of our primers, which prevents amplification of nonmetazoan taxa from complex eukaryote community samples, by enriching fauna associated with the marine brown algae Fucus vesiculosus. Our protocol will enable large-scale dietary analysis in metazoan filter feeders, facilitate aquatic food web analysis and allow surveying of aquacultures for pathogens. Moreover, we show that mussels and other aquatic filter feeders can serve as complementary DNA source for biomonitoring.